Reading GO enrichment object

en_body = readRDS(here::here('data/enGo_body.Rds'))

Level 3 blocks

goplot_list = llply(en_body$summary$Name[en_body$summary$Nested_Level==3],
                    XGR_plot, en_body$XGR, en_body$summary)
## [1] "0-2-0"
## [1] "1-1-1"
## [1] "2-0-0"
## [1] "3-0-0"
names(goplot_list) = en_body$summary$Name[en_body$summary$Nested_Level==3]

0-2-0 - Biological Regulation, Cell Cycle, Transcription

1-1-1 - Cell Respiration, Krebs Cycle, Translation, Muscle Development

2-0-0 - Catabolism, Mitocondrial translation, peptide metabolism, development

3-0 - Immune response, eggshell chorion assembly

Probing some interesting blocks

Cell Cycle, Regulation of macromolecules

0-0-2-0

## [1] "0-0-2-0"

Overall: Gorilla 0-0-2-0

  • 0 - regulation of cellular process, regulation of transcription, cell cycle process, mRNA splicing Gorilla
  • 16 - cell cycle process, chromatin organization, reproductive process, eggshell chorion gene amplification Gorilla
  • 23 - regulation of G2/M transition of mitotic cell cycle (weak) Gorilla
  • 56 - mitotic cell cycle phase transition, regulation of cyclin-dependent protein kinase activity Gorilla

6-0-2-0

## [1] "6-0-2-0"

Overall: Gorilla 6-0-2-0

  • 6 - regulation of cell cycle process, regulation of cellular metabolic process Gorilla
  • 8 - regulation of gene expression, regulation of metabolic process Gorilla
  • 11 - regulation of primary metabolic process Gorilla
  • 20 - regulation of biological process Gorilla

Development, biological regulation, metabolism

2-0-2-0

## [1] "2-0-2-0"

Overall: Gorilla 2-0-2-0

  • 2 - animal organ development, anatomical structure development, anatomical structure development, several tissue specific development, regulation of transcription, regulation of RNA biosynthetic process Gorilla
  • 15 - motor neuron axon guidance, [glial|stem] cell fate determination Gorilla
  • 26 - regulation of metabolic process Gorilla
  • 27 - developmental process, regulation of metabolic process Gorilla
  • 43 - regulation of RNA metabolic process, regulation of gene expression Gorilla

Cell Development and metabolism, in a different level 3 block

10-2-0-0

## [1] "10-2-0-0"

Overall: Gorilla 10-2-0-0

  • 19 - cellular metabolic process , protein catabolic process Gorilla
  • 28 - cell development, regulation of metabolic process Gorilla
  • 29 - negative regulation of translation, posttranscriptional regulation of gene expression, mRNA metabolic process Gorilla

8-2-0-0

## [1] "8-2-0-0"

Overall: Gorilla 8-2-0-0

  • 14 - biological regulation, actin filament polymerization Gorilla
  • 25 - positive regulation of cellular process, developmental process, regulation of growth, cell migration, cell differentiation Gorilla
  • 31 - negative regulation of biological process, regulation of signal transduction, regulation of cell communication Gorilla

Translation and Cell respiration (really mixed together!)

1-1-1-1

## [1] "1-1-1-1"

Overall: Gorilla 1-1-1-1

  • 1 - cytoplasmic translation, cellular macromolecule biosynthetic process Gorilla
  • 9 - cytoplasmic translation, ribosomal small subunit assembly Gorilla
  • 41 - respiratory electron transport chain, mitochondrial electron transport, NADH to ubiquinone Gorilla

11-1-1-1

## [1] "11-1-1-1"

Overall: Gorilla 11-1-1-1

  • 24 - respiratory electron transport chain, ketone biosynthetic process Gorilla
  • 40 - cytoplasmic translation, [peptide|amide] biosynthetic process, macromolecule biosynthetic process Gorilla
  • 44 - cytoplasmic translation, mitochondrial electron transport, cytochrome c to oxygen Gorilla
  • 52 - mitochondrial electron transport, ubiquinol to cytochrome c Gorilla
  • 53 - cytoplasmic translation, macromolecule biosynthetic process Gorilla

9-1-1-1

## [1] "9-1-1-1"

Overall: Gorilla 9-1-1-1

  • 18 - cytoplasmic translation Gorilla
  • 38 - oxidation-reduction process (weak) Gorilla
  • 42 - transmembrane transport (weak) Gorilla
  • 48 - tricarboxylic acid cycle Gorilla
  • 49 - ATP synthesis coupled proton transport Gorilla

Small molecule metabolism, muscle formation

7-1-1-1

## [1] "7-1-1-1"

Overall: Gorilla 7-1-1-1

  • 12 - proteolysis (weak) Gorilla
  • 17 - ion transport Gorilla
  • 37 - fatty acid biosynthetic and metabolic process , acyl-CoA metabolic process Gorilla
  • 39 - glutathione metabolic process Gorilla
  • 45 - myofibril assembly, mesoderm development, actomyosin structure organization Gorilla
  • 47 - Nothing! Gorilla

Egg shell and Immune response

Gorilla 12-3-0-0

Block summary table:

dplyr::select(en_body$summary, Nested_Level, Name, N_genes, Internal_degree, Assortatitvity,  p.adjust, n_enrich)